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5ACZ

Gaga-BF2*021:01 binding "GRAEEYGADTL" at 2.69Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections

Complex type

Class i with peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
Gaga-BF2*021:01
['A']
3. Peptide
GRAEEYGADTL
['C']

Species

Locus / Allele group

GAGA-BF2 / Gaga-BF2*021

Publication

Complex of a B21 Chicken Mhc Class I Molecule and a 11mer Chicken Peptide

Chappell, P.E., Roversi, P., Harrison, M.C., Kaufman, J.F., Lea, S.M.

Structure deposition and release

Deposited: 2015-08-19
Released: 2016-09-28
Revised: 2016-09-28

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Undecamer (11 amino acids)

Sequence: GRAEEYGADTL

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

Data provenance

MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.

Peptide neighbours

P1 GLY

LEU5
TYR168
TYR58
TYR156
GLU62
TYR7
CYS161
TRP164
 P10 THR

ASN76
THR140
LYS143
TRP95
TRP144
TYR149
ILE72
 P11 LEU

LYS143
TRP95
ILE79
ARG83
PHE120
VAL121
ASN76
LEU80
VAL93
ALA113
THR140
 P2 ARG

ARG9
TYR156
GLU62
ILE65
SER69
TYR7
ASP24
VAL66
ARG61
 P3 ALA

TYR156
ILE65
 P4 GLU

ILE65
ARG61
 P5 GLU

TYR149
 P6 TYR

GLY68
GLN64
ILE65
ILE72
SER69
 P7 GLY

TYR149
ILE72
TRP144
 P8 ALA

LEU153
TRP95
TRP144
TYR149
HIS111
 P9 ASP

HIS111
ARG9
ILE72
SER69
ASN76
TRP95
TRP144
ASN73

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

Data provenance

Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.

Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWT
        70        80        90
FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF
2. Class I alpha
Gaga-BF2*021:01
        10        20        30        40        50        60
MGSCGALGLGLLLAAVCGAAAELHTLRYIRTAMTDPGPGLPWFVDVGYVDGELFMHYNST
        70        80        90       100       110       120
ARRAVPRTEWIAANTDQQYWDRETQIVQGSEQINRENLDILRRRYNQTGGSHTVQWMSGC
       130       140       150       160       170       180
DILEDGTIRGYHQAAYDGRDFVAFDKGTMTLTAAVPEAVPTKRKWEEGGYAEGLKQYLEE
       190       200       210       220       230       240
TCVEWLRRYVEYGKAELGRRERPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAV
       250       260       270       280       290       300
RGQDAQSGGIVPNGDGTYHTWVTIDAQPGDGDKYQCRVEHASLPQPGLYSWRSGGGLNDI
       310       320
FEAQKIEWHENSSSVDKLAAALEHHHHHH
3. Peptide
GRAEEYGADTL

Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.

Downloadable data

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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 5ACZ assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5ACZ assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5ACZ assembly 1  
Peptide only [cif]
  1. 5ACZ assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5acz

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.